Hmm interesting discussion.
On the one hand, I do agree that it shouldn't really matter whether the protagonist is male or female, black, white or purple-with-yellow-polkadots, as long as the story is good and the protagonist fits in it (both with regards to background story and abilities).
On the other hand, when the progtagonist is human (in appearance), I think there are some biological expectations that should be taken into consideration. I don't mean that we should only have stereotypical people (please no), but I instinctively feel that a female characters abilities would focus more around intelligence or agility and less around strength, whereas a male character perhaps could be physically stronger. This should, however, not stop anyone from making a body-builder-type female protagonist, if that is, what the story demands